Patent Application
20240016920
The present disclosure relates to a vaccine against SARS-CoV-2 virus infection, and, especially, relates to a vaccine combination against SARS-CoV-2 virus infection comprising a DNA vaccine and an antigen peptide vaccine.
The COVID-19 pandemic has caused over 30 million cases including 1.2 million deaths globally (1). While public health measures such as social distancing has played important roles in controlling local outbreaks, the continued spreading of COVID-19 pandemic to additional populations including those living in remote and underdeveloped areas would only extend the future threat (2-6). In addition, new waves of transmissions are occurring in many countries even after the original outbreaks came down (7, 8). More definitive large scale public health measures like vaccines are the only hope to achieve the full global control (9-12).
Currently there are at least a dozen COVID-19 vaccines have entered Phase III clinical studies to establish their efficacy before the wide public use (13). Several leading candidates are using novel vaccine platforms such as viral vector (14-18) or mRNA (19-23) approaches. No human preventive vaccines using these approaches have been formally licensed with efficacy clinical studies in the past. One other major type of COVID-19 vaccines is the inactivated vaccine approach (24-28) which is linked to possible adverse events observed with such type of vaccines in the past (29, 30). There are also biosafety issues related to the need of producing large stocks of live SARS-CoV-2 viruses before inactivation. Overall viral vector, nucleic acid or inactivated vaccines are not considered highly immunogenic based on the past experience. At the same time, it is reported that SARS-CoV-2 infection may not lead to high level immune responses and some recovered patients may be re-infected again by the same virus (31-33). Therefore, it is highly desirable to develop COVID-19 vaccines that are highly immunogenic and the elicited immunity is long lasting.
In one aspect, the present disclosure provides a DNA vaccine for use in a subject against SARS-CoV-2 virus infection, which comprises a polynucleotide sequence encoding a polypeptide of the SARS-CoV-2 virus, wherein the polynucleotide sequence is codon optimized for expression in the subject.
In some embodiments, the polypeptide is the SARS-CoV-2 spike protein or comprises at least a conserved moiety of the SARS-CoV-2 spike protein.
In some embodiments, the polypeptide comprises the receptor-binding domain (RBD) of the spike protein.
In some embodiments, the subject is a human being.
In some embodiments, the DNA vaccine is a plasmid constructed from plasmid pSW3891.
In some embodiments, the polynucleotide sequence comprises a sequence of SEQ ID NO: 3 or 4.
In another aspect, the present disclosure provides a method for preventing or treating SARS-CoV-2 virus infection in a subject, which comprises administering to the subject an effective amount of an DNA vaccine, wherein the DNA vaccine comprises a polynucleotide sequence encoding a polypeptide of the SARS-CoV-2 virus, and the polynucleotide sequence is codon optimized for expression in the subject.
In some embodiments, the polypeptide is the SARS-CoV-2 spike protein or comprises at least a conserved moiety of the SARS-CoV-2 spike protein.
In some embodiments, the polypeptide comprises RBD of the spike protein.
In some embodiments, the subject is a human being.
In some embodiments, the DNA vaccine is a plasmid constructed from plasmid pSW3891.
In some embodiments, the polynucleotide sequence comprises a sequence of SEQ ID NO: 3 or 4.
In another aspect, the present disclosure provides a vaccine combination for use in a subject against SARS-CoV-2 virus infection, which comprises:
In some embodiments, the polynucleotide sequence is codon optimized for expression in the subject.
In some embodiments, the polypeptide is the SARS-CoV-2 spike protein or comprises at least a conserved moiety of the SARS-CoV-2 spike protein.
In some embodiments, the polypeptide comprises RBD of the spike protein.
In some embodiments, the subject is a human being.
In some embodiments, the DNA vaccine is a plasmid constructed from plasmid pSW3891.
In some embodiments, the polynucleotide sequence comprises a sequence of SEQ ID NO: 3 or 4.
In some embodiments, the antigen peptide comprises at least a conserved moiety of the SARS-CoV-2 spike protein.
In some embodiments, the antigen peptide comprises RBD of the spike protein.
In some embodiments, the antigen peptide is the S1 subunit of the spike protein.
In some embodiments, the antigen peptide comprises an amino acid sequence of SEQ ID NO: 7 or a functional variant with sequence identity of 80% or more to SEQ ID NO: 7.
In some embodiments, the DNA vaccine and the antigen peptide vaccine are co-formulated in a vaccine formulation or each formulated as a separate vaccine formulation, with a pharmaceutically acceptable vehicle.
In some embodiments, the DNA vaccine and the antigen peptide vaccine are formulated as a vaccine formulation suitable for co-delivery through intramuscular injection.
In another aspect, the present disclosure provides a method for preventing or treating SARS-CoV-2 virus infection in a subject, which comprises administering to the subject an effective amount of a DNA vaccine and an effective amount of an antigen peptide vaccine, wherein the DNA vaccine comprises a polynucleotide sequence encoding a polypeptide of the SARS-CoV-2 virus; and wherein the antigen peptide is an antigen peptide of the SARS-CoV-2 virus.
In some embodiments, the polynucleotide sequence is codon optimized for expression in the subject.
In some embodiments, the polypeptide is the SARS-CoV-2 spike protein or comprises at least a conserved moiety of the SARS-CoV-2 spike protein.
In some embodiments, the polypeptide comprises RBD of the spike protein.
In some embodiments, the subject is a human being.
In some embodiments, the DNA vaccine is a plasmid constructed from plasmid pSW3891.
In some embodiments, the polynucleotide sequence comprises a sequence as set forth in SEQ ID NO: 3 or 4.
In some embodiments, the antigen peptide comprises at least a conserved moiety of the SARS-CoV-2 spike protein.
In some embodiments, the antigen peptide comprises RBD of the spike protein.
In some embodiments, the antigen peptide is the S1 subunit of the spike protein.
In some embodiments, the antigen peptide comprises an amino acid sequence of SEQ ID NO: 7 or a functional variant with sequence identity of 80% or more to SEQ ID NO: 7.
In some embodiments, the DNA vaccine and the antigen peptide vaccine are co-formulated in a vaccine formulation or each formulated as a separate vaccine formulation, with a pharmaceutically acceptable vehicle.
In some embodiments, the DNA vaccine and the antigen peptide vaccine are co-administrated to the subject.
In some embodiments, the DNA vaccine and the antigen peptide vaccine are co-administrated to the subject at least 3 times.
In some embodiments, the DNA vaccine and the antigen peptide vaccine are administrated through intramuscular injection.
In another aspect, the present disclosure provides a vaccine kit, which comprises a container, the DNA vaccine or the vaccine combination described above within the container, and a label on or associated with the container that indicates that the DNA vaccine or the vaccine combination is for use in preventing or treating SARS-CoV-2 virus infection.
In another aspect, the present disclosure provides uses of the DNA vaccine or the vaccine combination described above in the preparation of a medicament for preventing or treating SARS-CoV-2 virus infection.
In another aspect, the present disclosure provides a medicament for use in preventing or treating SARS-CoV-2 virus infection, which comprises the DNA vaccine or the vaccine combination described above.
The combination of a DNA vaccine encoding the S protein and an antigen vaccine comprising the S1 subunit is able to confer a full protection against the SARS-CoV-2 virus infection.
Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by a person of ordinary skill in the art. Any methods, devices and materials similar or equivalent to those described herein can be used in the practice of the present invention. The following definitions are provided to facilitate understanding of certain terms used herein and are not meant to limit the scope of the present disclosure.
The articles “a” and “an” are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element.
As used herein, a “DNA vaccine” refers to a DNA molecule which comprises a DNA sequence encoding a protein antigen, and, after being administrated to a subject (e.g., a human being), leads to humoral (and cell-mediated) immune to the antigen in the subject. Generally, the DNA sequence encoding the protein antigen is operably linked to an expression control sequence, such as a promoter, or array of transcription factor binding sites. The expression control sequence directs transcription of the DNA sequence. The DNA vaccine may include both naked DNA vaccines, e.g., plasmid vaccine, and viral vector-based DNA vaccines that are delivered as viral particles. DNA vaccines afford advantages over conventional vaccines including ease of production, stability, and transport at room temperature.
As used herein, an “antigen peptide vaccine” refers to a protein antigen that will stimulate a host's immune system to make a humoral and/or cellular antigen-specific response. The antigen peptide contains one or more epitopes (either linear, conformational or both). Normally, an epitope will comprise between about 7 and 15 amino acids, such as, 9, 10, 12 or 15 amino acids. An antigen peptide can be obtained by various methods known in the art.
The term “expression” refers to the biological production of a product encoded by a coding sequence. In most cases, the coding sequence, is transcribed to form a messenger-RNA (mRNA). The messenger-RNA is then translated to form a polypeptide product which has a relevant biological activity. Also, the process of expression may involve further processing steps to the RNA product of transcription, such as splicing to remove introns, and/or post-translational processing of a polypeptide product.
“Codon optimization” or “codon optimized for expression” refers to modifying a DNA sequence for enhanced expression in the cells of a subject of interest, e.g., human, by replacing at least one, more than one, or a significant number, of codons of the native sequence with codons that are more frequently or most frequently used in the genes of that subject.
A “conserved moiety” of a protein refers to a protein fragment that is conserved across a protein that may have high sequence diversity in nature, e.g., a viral protein. The conserved moiety needs not have 100% sequence identity across the diversity of naturally occurring sequence of the protein, but the sequence variability in the naturally occurring sequences is low, e.g., less than 10% or 5%.
A “functional variant” of an amino acid sequence refers to any variant exhibiting one or more functional properties identical or similar to those of the amino acid sequence with which it is compared, e.g., it is a functional equivalent. With respect to an antigen peptide, one particular function is the ability to elicit the production of neutralizing antibodies against a virus, when administered to a mammalian subject. In some embodiments, such functional variants may have at least about 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, 99% or more of the activity of the antigen peptides with a sequence as set forth in SEQ ID NO: 7, when measured using standard tests recognized by those of skill in the art. Functional variants may include peptides which have changes or mutations (e.g., at least about one, two, or four, and/or generally less than 15, 10, 5, or 3) relative to the sequence described herein (e.g., conservative or non-essential amino acid substitutions), which do not have a substantial effect on peptide function. Whether or not a particular substitution will be tolerated, i.e., will not adversely affect biological properties, can be predicted, e.g., by evaluating whether the mutation is conservative.
“Vaccine combination” refers to a combination of a DNA vaccine and an antigen peptide vaccine which are administrated to the same subject to elicit an immune response. In some embodiments, the DNA vaccine and the antigen peptide vaccine are co-formulated in a single vaccine formulation with a pharmaceutically acceptable vehicle. In other embodiments, the DNA vaccine and the antigen peptide vaccine are each formulated as a separate vaccine formulation with a pharmaceutically acceptable vehicle.
In embodiments where the DNA vaccine and the antigen peptide vaccine are separate vaccine formulations, the DNA vaccine and the antigen peptide vaccine can be administrated to the subject simultaneously (i.e., co-administrated) or sequentially.
As used herein, “administrated simultaneously”, “co-administrated” or “co-delivered” means that the DNA vaccine and the antigen peptide vaccine are administrated to the same subject at the same time or at substantially the same time. For example, the DNA vaccine is administrated firstly, and, within 1 hour, 1 day, or 2 days, the antigen peptide vaccine is administrated. In these cases, the antigen peptide vaccine is often administrated before the firstly administrated DNA vaccine is able to induce an effective immune response in the subject. This administration scheme is therefore different from the “prime-boost” approach. By contrast, “administrated sequentially” means two vaccines are administrated at different times in which the response to the first vaccine is boosted by a second vaccine comprising the same or different antigen than the first vaccine.
As used herein, “treatment” or “treating” includes any actions which may lead to any beneficial or desirable effect on the symptoms or pathology of a disease (or disorder) in a subject, even minimal reductions in one or more measurable markers of the disease being treated. “Treating” can optionally involve delaying of the progression of the disease. “Treatment” does not necessarily indicate complete eradication or cure of the disease, or associated symptoms thereof.
As used herein, the term “prevention” or “preventing” involves the implementation of necessary practices to prevent the occurrence of a disease or reduce the possibility of the occurrence of a disease in a subject. It does not imply that the disease will not occur.
As used herein, the term “subject” refers to an organism to which the vaccine(s) of the present invention will be administered. Preferably, a subject is a bird or a mammal, e.g., a human being, primate, livestock animal, or a rodent.
The vaccine(s) of the present invention can be used as pure compound, or can be formulated with a pharmaceutically acceptable carrier to form a vaccine formulation. Pharmaceutically acceptable carriers are well known in the art and include, for example, aqueous solutions such as water or physiologically buffered saline or other solvents. In preferred embodiments, when such pharmaceutical compositions are for human administration, e.g., for parenteral administration, the aqueous solution is pyrogen-free, or substantially pyrogen-free.
The route of administration of the vaccine(s) of the present invention may be by parenteral, subcutaneous, intravenous, intramuscular, intraperitoneal, intraarterial, intralesional, intraarticular, topical, oral, rectal, nasal, or any other suitable route.
An “effective amount” of the vaccine(s) of the present invention for preventing or treating SARS-CoV-2 virus infection may vary according to factors such as the disease state, age, sex, and weight of a subject (e.g., a patient). The precise amount contemplated in particular embodiments, to be administered, can be determined by a physician in view of the condition of the subject.
In the current study, we developed a novel subunit COVID-19 vaccine including the S full length DNA plasmid and S1 recombinant protein co-delivered at the same time. This design is most effective in eliciting the higher immune responses including protective antibody and T cell responses than using either DNA or protein component alone. More significantly, this novel COVID-19 vaccine design was able elicit a full protection against the challenge of SARS-CoV-2 in an NHP model (e.g., Rhesus Macaque) which has not been easy to achieve by previous COVID-19 vaccine studies in similar NHP models.
Some embodiments of the present invention are at least partially based on the surprising findings that, the wild type DNA sequences encoding the S protein do not elicit an S-specific antibody responses, while codon optimized DNA sequences encoding the same protein (or its truncated soluble form) are able to elicit a significant S-specific antibody response. Some embodiments of the present invention are at least partially based on the surprising findings that, a combination of a DNA vaccine encoding the S protein and an antigen vaccine comprising the S1 subunit is able to confer a full protection against the SARS-CoV-2 virus infection in NHP model studies.
The wildtype (S-FL-wt) and codon optimized SARS-CoV-2 spike protein (SEQ ID NO: 1) full length gene sequence (S-FL-opt) were commercially synthesized based on the Wuhan-Hu-1 (GenBank:MN908947). The soluble S ectodomain insert sequence (S-dTM-opt) was generated from the full length opt sequence using the oligomers w1404-TACCGAGCTCGGATCCGCCACCAT (SEQ ID NO: 12) and w1406-GATATCTGCAGAATTCTCAAGGCCACTTGATGTACTGCTCG (SEQ ID NO: 13). All three inserts (S-FL-wt (SEQ ID NO: 2), S-FL-opt (SEQ ID NO: 3) and S-dTM-opt (SEQ ID NO: 4)) were individually subcloned into the mammalian expression plasmid pcDNA3.1+ between BamHI and EcoRI by In-Fusion cloning technology (TAKARA Bio, China). These S-expressing DNA vaccine plasmids were purified from E. coli (TAKARA Bio, China) using endotoxin-free plasmid Maxi kit (Qiagen, USA). All plasmid sequences were confirmed by Sanger DNA sequencing.
The DNA vaccine pCW1093 was produced by subcloning the S-FL-opt insert into the DNA vaccine vector pSW3891 which can be used in humans as previously reported (34). The insert was amplified from the S-FL-opt template by using the oligomers w1477-TCCATGGGTCTTTTCTGCAGTCACCGTCCAAGCTTGCAATCGCCACCATGTT CGTGTTCCT (SEQ ID NO: 5) and w1479-GGGATTGCGAGGATCCTTATCATGTGTAGTGGAGCTTCACG (SEQ ID NO: 6) and fused into linearized pSW3891 at PstI and BamHI sites. The pCW1093 plasmid (
Codon optimized version of gene sequence encoding for S1 protein (SEQ ID NO: 7) was subcloned into the mammalian expression vector for in vitro production of recombinant S1 protein for research study applications, and a His-tag was added to the C-terminal of S1 protein for purification purpose. The Expi293 cells (Invitrogen, US) were transfected with the S1-expressing plasmid, the supernatant of cell culture was harvested on Day 5 and the S1 protein was purified by HisTrap HP column. The quality was verified by SDS-PAGE and Western blot analysis before being used for immunization and ELISA study purposes. For immunization, S1 protein was absorbed with aluminum hydroxide (Brenntag Biosector, Frederikssund, Denmark) at a ratio of 1:3.5 (w/w).
S-expressing DNA vaccines were tested for their in vitro expression in transiently transfected 293T cells using PEI as the transfecting agent as previously reported (35). 72 hours after the transfection, culture supernatants or cell lysates were subject to Western blot analysis with a rabbit polyclonal serum L295-IV specific for S protein of SARS-CoV-2 virus as the detecting antibody. Similarly, recombinant S1 protein purified from Expi293 cell production was tested with western blot using the same rabbit polyclonal serum.
Pilot animal DNA immunization studies were conducted in mice and non-human primates to compare the relative immunogenicity of different S-expressing DNA vaccine constructs (S-FL-wt, S-FL-opt and S-dTM-opt). Either 6-8 weeks old C57BL/6N mice or 3-4 years old rhesus monkeys were immunized three time at Weeks 0, 2 and 4 with 5 μg DNA each time delivered by a Helio Gene Gun (Bio-Rad, USA). Serum samples were collected prior to the start of the study or 14 days after each immunization.
Additional pilot study was conducted in New Zealand White (NZW) rabbits. Rabbits were either immunized with DNA vaccines (S-FL-opt) three times (Weeks 0, 2 and 6) with 200 μg DNA vaccine each time by needle intramuscular injection (IM), or received twice IM DNA immunizations (S-FL-opt or S-dTM-opt) at Weeks 0 and 2, followed by one time IM injection of 50 μg recombinant S1 protein vaccine at Week 6. Serum samples were collected prior to the start of the study or 14 days after the 3rd immunization.
The relative immunogenicity of different vaccination designs (S-FL-opt DNA alone, S1 protein alone or co-delivery of S-FL-opt DNA+S1 protein vaccines) was further studied in NZW rabbit. All animals received three intramuscular (IM) needle immunizations at Week 0, 2 and 6 with fixed dosing: 200 μg DNA vaccine and 50 μg protein vaccine, delivered either alone or in combination. Serum samples were collected prior to the start of the study or 14 days after the 3rd immunization.
Groups of randomly assigned 3-4 years old rhesus monkeys were immunized three times at Weeks 0, 2 and 8 with one of the following vaccination regimen: DNA vaccine pCW1093 (2 mg each time), recombinant 51 protein (100 μg each time) or co-delivery of DNA vaccine pCW1093 (2 mg) and 51 protein (100 μg) each time, all delivered by intramuscular needle injections. The control animals received saline injections. Peripheral blood was collected prior to the start of study and 7 days after each immunization for routine blood biochemical tests and SARS-CoV-2 specific immune responses.
A challenge study was conducted at 4 weeks after the third immunization by direct inoculation of 5×106 TCID50 of SARS-CoV-2 virus through the intratracheal route under anesthesia. Throat and anal swabs were collected at 0, 2, 4, 6 and 7 days after challenge and used to determine the viral load. At seven days after challenge, all animals were euthanized, the viral load in the different tissue was detected, and a pathological examination was conducted.
SARS-CoV-2 strain BP16 was isolated from the sputum of a COVID-19 patient in Kunming, Yunnan, and amplified in Vero cells. The viral genome was extracted and subjected to nanopore sequencing (Nextomics Bioscience, Wuhan). The BP16 complete genome contains two mutations, C8782T and T28144C aligned with Wuhan-Hu-1. The former is a silent mutation, and the latter resulting in an amino acid difference in the ORF8 (L84S). BP16 was used in the neutralization and challenge assay. Vero cells were used for the production and titration of SARS-CoV-2 stocks. Vero cells were maintained in Dulbecco's modified Eagle's medium (DMEM, Corning) supplemented with 10% fetal bovine serum (FBS, Gibco,) 100 IU/mL penicillin, and 100 μg/mL streptomycin, and incubated at 37° C., 5% CO2. The SARS-CoV-2 virus titer was determined by a micro-dose cytopathogenic efficiency (CPE) assay. Serial 10-fold dilutions of virus-containing samples were mixed with 2×104 Vero cells and then plated in 96-well culture plates. After 5 days of culture in a 5% CO2 incubator at 37° C., cells were checked for the presence of a CPE under a microscope. Titers for SARS-CoV-2 were resolved by a 50% tissue-culture infectious doses (TCID50) assay.
The 96-well ELISA plates (Corning, USA) were coated with 0.2 μg/well S1 protein in 100 μL coating buffer (15 mM Na2CO3 and 35 mM NaHCO3, pH 9.6) and incubated at 4° C. overnight. Plates were washed in PBST (0.5% TWEEN-20/PBS) and wells blocked using 2% BSA/PBST for 1 hr at 30° C. Serially diluted serum samples were added and incubated for 1 hr at Plates were washed and horseradish peroxidase-conjugated goat anti-mouse IgG or anti-rabbit IgG (Invitrogen, USA) or horseradish peroxidase-conjugated goat anti-monkey IgG (Santa Cruz Biotechonology, USA) was added to all wells for 1 hr at 30° C. The reaction was developed using TMB substrate (Makewonderbio, Beijing, China) and determined at 450 nm by a microplate reader.
Two neutralization assays were used in the current report. The first one was conducted at IMB based on the neutralizing activities against real SASR-CoV-2 virus infection to Vero cells. In this assay, mouse or NHP serum samples collected from immunized animals were heat-inactivated at 56° C. for 30 min and serially diluted with virus dilution medium at a starting dilution of 1:4 and then serially diluted 2-fold up to the required concentration. An equal volume of challenge virus solution containing 100 TCID50 virus was added, followed by 1 hour incubation at 37° C. 1×104 Vero cells were then added to the serum-virus mixture, and the plates were incubated for 5 days at 37° C. in a 5% CO2 incubator. Cytopathic effect (CPE) of each well was recorded under microscopes, and the neutralizing titer was calculated by the dilution number of 50% protective condition.
The second neutralization assay is a pseudotyped virus based assay conducted at UMMS. The heat-inactivated immune rabbit serum samples were serially diluted at a starting dilution of 1:20 with 2-fold serial dilutions in 55 μl of volume. An equal volume of SARS-CoV-2 pseudovirus (100 TCID50/mL) was added, followed by 1 hour incubation at 37° C. Then take 100 μl of the serum/virus mixture and add it to the 96 well plates proceeded with 1×104 Vero-E6 cells per well. After the plates were incubated for 24 hours at 37° C. with 5% CO2, 100 μl/well fresh media was fed. At 48 hours after the infection, cells were washed with PBS and then lysed using passive lysis buffer. The luciferase activities developed with Luciferase substrate (Promega) and read. Neutralization was calculated as the percent change in luciferase activity in the presence of preimmune sera versus that of luciferase activity in the presence of immune sera [(Preimmune RLUs−Immune RLUs)/(Preimmune RLUs)]×100. The NAb titers were determined at the serum dilution with 50% neutralization.
Immunized macaque PBMCs were isolated to evaluate the antigen-specific T cell responses by ELISpotPLUS (ALP) kits (Mabtech, Sweden). The ELISPOT plates were incubated with 200 μl/well of serum-free media for 30 minutes at room temperature. Then add 50 μl/well of pooled peptides (5 μg/peptide/mL) or S1 protein (20 μg/mL) in serum-free media and 50 μl/well of macaque PBMCs at 3×105 cells/well. The plates were incubated for 16 hours at 37° C. with 5% CO2. After the plates were washed with pre-chilled water and PBS for 5 times, the plates were detected with conjugated anti-cytokine antibodies.
For macaque IFN-γ detections, biotinylated-anti-monkey IFN-γ at 1:1000 dilution in PBS with 0.5% FBS was added at 100 μL/well and incubated for 1 hour at room temperature. Following washes, the plates were further incubated with 100 μl/well of ALP-conjugated-Streptavidin at 1:1000 dilution for 1 hour at room temperature. Following washes with PBS for 5 times, the plates were developed with 100 μl/well of BCIP/NPT-plus substrate for 5 minutes in dark and washed with water and air-dried. For macaque IL-4 detection, the plates were directly incubated with 100 μl/well of ALP-conjugated-anti-human-IL-4 at 1:1000 dilution for 1 hour at room temperature. Following washes with PBS for 5 times, the plates were developed with 100 μl/well of BCIP/NPT-plus substrate for 5 minutes in dark and washed with water and air-dried. The immune spots in the ELISPOT plates were counted using ELISAPOT reader (CTL, USA) and the final sport-forming units (SFUs) were calculated as spots/million cells.
Tissues were homogenized in TRNzol universal reagent by TGrinder H24 (TIANGEN, China) and RNA was extracted using Direct-Zol RNA Miniprep kit (ZYMO RESEARCH). Viral gRNA was reverse transcribed and amplified by One Step PrimerScript RT-PCR Kit (TakaRa) using Ligtcycler 480II Real-Time PCR System (Roche) according to manufacturer's instructions. Viral loads were calculated as viral RNA copies per mL or per mg tissue and the assay sensitivity was 100 copies. The target for amplification was SARS-CoV2 N (nucleocapsid) gene. The primers and probes for the targets were:
For quantification of viral loads by RT-PCR, A standard curve of Ct values to the copy number of viral RNA is generated with serial 10-fold dilutions of RNA transcribed from recombinant plasmid pcDNA3.1-nCoV N in vitro with a known copy number. The viral loads of each sample were converted with Ct value and the standard curve. Statistical analysis was performed by LightCycler 480 Software.
The collected tissue sections (3 mm thickness) were fixed with 4% formaldehyde for 1 week. The fixed tissues were further dehydrated before being sliced into 2-3 μm thickness sections, and flatten on slides in warm water (40° C.). The slides were further dried and dewaxed at 60° C., and were stained with hematoxylin for 3-5 min, differentiated with hydrochloric acid aqueous solution, blue with aqueous ammonia solution, stained with eosin for 5 min after dehydration. The slides were finally sealed with neutral gel.
Analysis of virologic and immunologic data was performed using GraphPad Prism 8.4.2 (GraphPad Software). Comparison of data between groups was performed using two-sided Mann-Whitney tests. Correlations were assessed by two-sided Spearman rank-correlation tests. Student t-test was used to compare the antibody titers between groups. P-values of less than 0.05 were considered significant.
The current study is designed based on the significant amount of information accumulated in the literature in the last 2 decades including our own work that the immunogenicity of DNA vaccines is limited when used alone (36-38), even with the inclusion of molecular adjuvants such as plasmids expressing immune enhancing cytokines (39, 40). Physical delivery approaches such as gene gun and electroporation can greatly enhance the immunogenicity but the cost and complexity are increased with the use of a physical instrument. One promising option is the heterologous prime-boost or co-delivery of DNA vaccine with another vaccine modality such as recombinant protein vaccines which share the same antigens with the ones expressed by DNA vaccines (41-44).
We have adopted the same concept in the current study to test whether a combination of DNA and protein COVID-19 vaccine can greatly enhance the protective immunogenicity than using either DNA or protein components alone.
The optimal design of DNA vaccine expressing the S protein of SARS-CoV-2 as the key protective antigen was selected after comparing the immunogenicity of two similar versions of candidate S DNA vaccines. The first one, S-FL-opt, is the full length S gene insert expressing the exact same amino acid sequences as the natural S protein from the SARS-CoV-2 virus (
The relative immunogenicity of S-FL-opt and S-dTM-opt DNA vaccines was studied in multiple animal models. First in Balb/C mice using gene gun delivery, both S-FL-opt and S-dTM-opt DNA vaccines elicited S-specific serum antibody responses and the titers went up following each immunization with the same DNA vaccines (
Then in a pilot non-human primate (NHP) study using gene gun delivery, both the temporal development and the peak level of serum S-specific IgG titers in S-FL-opt group were significantly higher than in S-dTM-opt group (p<0.05) (
With the identification of the most optimal S-expressing DNA vaccine design, a recombinant S1 protein was produced in parallel from transiently transfected Expi293 cells so it can be used to test the DNA and protein combination vaccine strategy. The design of S1 protein gene is shown in
An immunogenicity study was conducted in NZW rabbits to test the immunogenicity of DNA and protein combination vaccine design. Both DNA and protein vaccines in this study were delivered by the traditional needle intramuscular injection (IM). Animals were immunized either with the S-FL-opt DNA vaccine alone, or with a S1 protein boost after priming with one of the two S DNA vaccines (S-FL-opt or S-dTM-opt). The result clearly demonstrated that the protein boost is highly effective in eliciting much higher S-specific IgG responses than giving DNA vaccine alone. The protein boost was able to push the antibody titers in animals primed with the less optimal DNA vaccine S-dTM-opt higher than those only receiving the optimal DNA vaccine S-FL-opt alone. However, after the S1 protein boost, the titers in those primed with the optimal DNA vaccine S-FL-opt were still higher than those primed with the less optimal DNA vaccine S-dTM-opt (
We next tested the relative immunogenicity between the sequential and the co-delivery of full length S-expressing DNA and S1 protein vaccines in the NZW rabbit model. The co-delivery immunization schedule is reported to be highly immunogenic (51) and is easier to implement in large human populations without tracking when a DNA or a protein vaccine component should be administered as in a sequential prime-boost design. Rabbits receiving the co-delivery of DNA and protein vaccines were able to induce much higher S-specific IgG responses than the DNA alone group, but only slightly better than the protein alone group (
Based on the results of from the above pilot animal studies, the co-delivery of DNA and protein vaccines approach was selected as the leading immunization design of our candidate COVID-19 vaccines and further tested in an NHP protection study against live SARS-CoV-2 viral challenge. As seen in the preliminary rabbit study, co-delivery of S-FL-opt DNA vaccine and recombinant S1 protein vaccine was the most immunogenic design to elicit higher S-specific IgG responses than DNA alone or protein alone groups (p<0.05 in both cases) (
Animals in this NHP study were further challenged with the live SARS-CoV-2 virus through the intratracheal route. The co-delivery of S-FL-opt DNA and recombinant S1 protein vaccines achieved the full protection. No virus was detected in trachea, lung lymph tissues and lung tissues in this group of animals (
A safe and efficacious SARS-CoV-2 vaccine is needed to end the global COVID-19 pandemic. Multiple vaccine candidates have advanced to Phase III human efficacy trials with some of them are expected to receive regulatory approval in near future for possible use in certain high risk populations. However, very little is currently known about the real protection efficacy of these leading vaccine candidates and more importantly how long the immune protection may last with these candidates. It is prudent to develop the next generation of vaccines which will be able to elicit stronger immune responses and better protection against SARS-CoV-2 viral infection than the first generation of COVID-19 vaccines under development.
In this study, we analyzed the relative immunogenicity of DNA, protein and the combination of DNA and protein vaccines. We demonstrated while codon optimization and optimal S gene insert design may produce the more immunogenic S-expressing DNA vaccines as previously reported (57), the combination of DNA and protein together can significantly improve the overall anti-S antibody responses and specifically the NAb responses than the DNA or protein vaccines alone approaches. Both the sequential DNA prime-protein boost and co-delivery of DNA and protein components at the same time are similarly effective in eliciting high level protective antibody responses, indicating the value of DNA vaccine in generating antibodies against conformation sensitive epitopes (52, 53). Co-delivery approach may be more practical for large scale human population applications as the vaccine formulation will be same for each time of immunization and no need to worry whether a DNA or protein vaccine should be administered as in the sequential prime and boost regimen.
By using the co-delivery of DNA and protein vaccines approach, we demonstrated that it can elicit full protection in all monkeys receiving such a combination vaccine formulation without any detectable viruses in all studied tissues compared with sham control animals. Both DNA vaccine alone or protein vaccine alone approaches achieved viral load reduction in various tissues as reported by other current COVID-19 vaccines but not full protection in any of the immunized monkeys in these two groups.
Our data extend previous studies showing the DNA and protein combination vaccines are more effective than either component alone in eliciting potent immune responses against HIV-1 or influenza (36, 37, 42). DNA immunization can use both innate immunity and acquired immunity mechanisms as we reported (58-61) to induce the development of antigen specific B cell responses especially those germinal center B cells which is the basis for much amplified antibody responses upon the boost of a protein vaccine. It is now known that SARS-CoV-2 infection does not establish long lasting antibody responses in patients who had mild clinical symptoms indicting the potential low immunogenicity of its S antigen. Such findings imply that a successful COVID-19 vaccine needs to elicit stronger than the natural infection, and a long-lasting immune responses including a long-lasting S-specific memory B cells may be critical. Our approach including the DNA component will greatly facilitate this process. More significantly, the inclusion of a DNA vaccine component can serve two important purposes: 1) to improve the quality of antibody responses such as the levels of NAb, due the ability of DNA vaccines to induce better antibody responses against conformational epitopes (52, 53) and 2) to elicit high levels of antigen specific memory B cells through better activation of germinal center B cell development than protein based vaccines (60, 61).
However, as shown in this study again, the immunogenicity of even optimized DNA vaccine still has its limits on how high the antibody responses may be elicited, and the addition of a protein vaccine can further push the limit higher. Low immunogenicity is a common feature for all kinds of nucleic acid vaccines including both DNA and RNA vaccines when used alone. As we learned in the last two decades, strategies such as enhanced delivery, using immune stimulating cytokines or adjuvants, and physical delivery tools (gene gun or electroporation) can only partially improve the immunogenicity of nucleic acid based vaccines (62) and may also bring additional issues such as safety, cost and complexity of use. The combination DNA and protein vaccine strategy offers a unique solution to maximize the efficacy of two vaccine modalities without causing any additional safety concern (41, 63). While we focused on the prime-boost approach in the past, our current data proved that co-delivery of DNA and protein vaccines at the same time could also produce higher immune responses and enhanced vaccine protection against SARS-CoV-2 in a non-human primate model The DNA and protein combination formulation should be considered as a leading candidate for the next generation of improved COVID-19 vaccines if a high immune responses and long lasting immunity are needed to achieve the full control of COVID-19 from a global scale.
Listed below are some amino acid sequences and nucleic acid sequences mentioned herein.
| Number | Date | Country | Kind |
|---|---|---|---|
| PCT/CN2020/131098 | Nov 2020 | WO | international |
This application claims priority to PCT patent application PCT/CN2020/131098, filed Nov. 24, 2020, the content of which is incorporated herein by reference.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CN2021/132703 | 11/24/2021 | WO |
